India Opal Buloni was picking up a few groceries from a Winn-Dixie grocery store when she saw the store manager chasing an apparently stray dog around the produce department. Opal (as she is known) overhears him asking someone to call the pound, and unable to stand the idea of such a smiley, friendly dog being taken there she says that the dog is hers. Calling him Winn-Dixie - the first name that pops into her head - she takes him home to Friendly Corners Trailer Park and asks her father, the local preacher, if she can keep him. Although he tells her that she doesn't need a dog, Opal tells him the dog needs her, and when she whistles for him to come in, he does so. His ribs are visible, his fur is matted and he even has some bald patches. The preacher realizes this is a dog on need and tells him that he has found a home. Joyfully, Opal begins cleaning him up immediately. She talks to him all the time she is brushing out his fur and feels like he is really listening, and understanding what she says. She tells him that she has no friends in town because she just moved a d all of her friends are back up in North Florida. She tells him about her mother, who left them, and how much she thinks about her. He listens and even seems to look at Opal as if he understands. After a while Opal is finished grooming him and re-introduces him to her father. She also asks him to tell her ten things about her mother so that if she should see her again sometime, she would know enough about her to be able to recognize her. He agrees but talking about his wife upsets him and so he doesn't line to do if very often.
They discover Winn-Dixie hates to be left alone when they leave together and tie him up outside the trailer until they return. He howls and howls but when they leave him in the trailer he destroys the couch and pulls all the toilet paper off the roll. They decide that they will always take him with them wherever they go. This includes the Open Arms Baptist Church where Opal's father is the preacher. As the preacher is talking Winn-Dixie sees a mouse run across the floor, and catches it, holding it in his mouth unharmed and giving it to the preacher.
Once his fur starts growing in, and he looks more healthy and well-fed, Opal decides he needs a nice collar and leash and goes to Gertrude's Pets to buy one. The red leather collar and leash she finds is very expensive so she asks the young man at the counter if she can pay in installments. He is dubious because the owner wouldn't like it, so Opal offers to work for him, sweeping and doing other jobs as needed, until she has earned enough to pay off the collar and leash. She even persuades him to let Winn-Dixie come inside the store. It strikes Opal that she is making quite a few new friends because if Winn-Dixie, like Otis, the clerk at Gertrude's Pets, Miss Franny Block, the older lady who presides over the Herman W. Block Memorial Library, and Sweetie Pie Thomas who loves dogs and invites Opal to her sixth birthday party. He is also the reason she meets Gloria Dump. She and Winn-Dixie are coming home from the pet store, Opal riding her bicycle and Winn-Dixie running along beside her. As they pass Dunlap and Stevie Dewberry's house they get on their bikes too and follow her. Opal doesn't like the Dewberry boys as they are mean to her, and she likes them even less when they tell her Winn-Dixie is headed for the witch's house. Despite her calling him back, Winn-Dixie disappears into the incredibly overgrown yard, and although she is scared by the possibility of running into a real-life witch she is more scared of losing Winn-Dixie and follows him into the jungle of a yard. She spots him around the side of a huge tree sitting by an old lady with no teeth. Gloria Dump introduces herself and offers Opal a peanut butter sandwich. She also wants to know everything about Opal so that even though her eyesight is too poor to really see her, she will be able to see her with her heart. Opal tells her everything, from how she and the preacher just moved to town to how the Dewberry boys say Gloria is a witch. Gloria teaches Opal how to plant a tree and Opal cannot wait to visit again. That night, there is a bad thunderstorm during which they discover that Winn-Dixie has what the preacher calls a pathological fear of thunder. He runs the length of the trailer over and over again and although Opal is worried this he will make the preacher reconsider keeping him, it does not - it merely means they have to make sure to take care of him in a storm so he never runs off.
Opal and Winn-Dixie are so early for work the next day that the closed sign is still on the door. The door is actually open so she goes inside but before she can call our to Otis to let him know they have arrived she hears the prettiest music she has ever heard and discovers all of the animals out of their cages listening to Otis play his guitar. Winn-Dixie is just as captivated as the other animals and all is calm until Gertrude, the parrot, sees Winn-Dixie and flies over to land on his head. Suddenly all the animals are moving and Opal and Otis run around the store trying to catch them without alot of success; after a while Opal realizes that Otis' music calms them down so he plays again and they manage to catch the rest of the "pets" and return them to their cages.
When she tells Gloria that Otis has been in jail and that has probably done some bad things, Gloria takes her to the back of the yard and shows her the mistake tree. All sorts of empty liquor bottles hang from the tree, each one a mistake Gloria has made in her life. She tells Opal that it is what a person is like in the present that matters, not what they did in the past. Once again it makes Opal think of her mother and wonder if her mother ever thinks of her.
Opal decides to visit Miss Franny at the library and get a book that she can read aloud to Gloria. Miss Franny suggests "Gone With The Wind" and proceeds to tell Opal about her great-grandfather, Littmus W. Block, who was a soldier in the civil war. As Opal is settling down with Winn-Dixie for the story, the library door bangs and Amanda Wilkinson, a girl of Opal's age whom Opal finds unfriendly, walks in. Pretending f not to be interested, she also listens to the story. They hear how Littmus was barely more than a bit when the war began but he enlisted anyway. After the was he returned home to find his home had been burned to the ground and his sisters had dies of typhoid. His parents were both dead as well and Littmus missed everyone so badly he sat down and cried. He also really wanted to eat something very sweet and decided there and then that the world had enough ugliness in it and that he was going to make candy. He created the Littmus Lozenge, which is sweet and delicious, but always makes the person eating it feel a little bit sad.
Opal takes a lozenge to Otis the next day and asks him why he was in jail. He admits he was playing his guitar in the street and when people gave him money to show appreciation the police moved him on. They tried to handcuff him and frustrated about not being able to play his guitar, he hit one of the police officers. After he was released from jail he was told not to play guitar in the street again, which is why he only plays in the pet store. When she tells Gloria what he was jailed for Gloria laughs and teases Opal about working with such a dangerous criminal. As they read the chapter of "Gone With The Wind" that describes the barbecue Scarlett O'Hara, the main character, is throwing, Opal decides to throw a party at Gloria's home, only instead of barbecue they will serve egg salad sandwiches. Gloria says they can have a party on condition that Opal invites the Dewberry boys. Opal invited Miss Franny, who tells her to invite Amanda, and she also invites Sweetie Pie Thomas and Otis, as well as her father. The day of the party is hugely exciting and Opal is happy that she can finally introduce all of her friends to each other. Before they eat, the preacher says grace to bless the food, and everything is going well - until there is a rumble of thunder. Scooping up the food it is only after they have run inside that Opal realizes they have lost sight of Winn-Dixie. Panicked, she and her father go out into the pouring rain searching. They search everywhere but have no luck, and Opal is angry because she thinks he has given up on Winn-Dixie just like he gave up on her mother. He tells her that he never gave up but that he knows she will never come back; despite how much pain this causes him he still feels blessed because he has Opal.
They hear music before they get back to Gloria's house and return to find Otis playing his guitar with everyone smiling and having a great time. Opal shouts that they didn't find him and Gloria tells her that's because he was in the house all the time; he had run under the bed in her room. The rain stops outside and Opal walks out to Gloria's mistake tree, talking aloud to her mother and telling her that she doesn't feel as empty inside as she used to. Dunlap is waiting for her and challenges her to a race back to the house. Opal wins and also wins the beginning of a real friendship with Dunlap. They ask Otis to play some hymns and as Opal looks around her, with her father on one side and Amanda on the other, she knows that she has friends, and is really rather happy, because of Winn-Dixie.